Rapid advances in DNA technology have created a swell of new products and therapies through biotechnology, but the greatest gap in our ability to manipulate biological systems has been in the area of controlling gene expression. Specifically, despite our understanding and mapping of nearly all gene coding regions in human and several other species, we cannot ‘decode’ the DNA sequence that lies upstream of a gene, called the promoter. Enhancer binding proteins (subsequently referred to as transcription factors) bind to these regions, typically more than a dozen different ones bind to each and every gene promoter. How these factors work together to so precisely control the expression of genes has remained unsolved.
At stake is having predictive power of when a gene will be turned on or off based on assessment of the gene specific transcription factors present in a living cell at any given time, and in response to any treatments, including drugs. Also, the ability to alter gene expression or create promoters starting with individual transcription factor binding sites has been greatly impaired because one cannot ‘read’ what these factors are doing.
Currently, despite identifying many individual transcription factors, and in some cases having cloned them to know their exact amino acid sequences, how these factors help to catalyze transcription is not known. The current thinking is turning towards alterations in chromatin structure mediated by transcription factors possessing histone acetylase or deacetylase activity, yet most of the transcription factors positioned upstream of an eukaryotic gene do not have these activities.
Much work in the past in the transcription field has been focused on the role of so called ‘general transcription factors’ (GTFs), i.e., those factors required by all promoters to achieve gene transcription (see, for example, the work of Roeder, Sharp, Tjian, and Reinberg). The upstream binding transcription factors that control transcription rates have been presumed to interact with the components of the general transcription complex. In the dominant paradigm, a direct interaction between these upstream transcription factors and the GTFs presumably occurs by looping out of the intervening DNA. Yet during the decade that this model has dominated, it has not helped to illucidate further the role of upstream factors.
Prokaryotes (i.e., bacteria) have served as a model for eukaryotic transcription and it is presumed that the same set of transcription steps is likely involved in both systems. However, eukaryotes have many more genes regulated in more complex patterns and so may require a unique additional level of gene regulation. Specifically, eukaryotes employ transcription factors that enhance expression from distances of over a thousand base pairs away from the initiation site of transcription. Prokaryotes do not have this class of transcription factors and so do not provide a reliable model for understanding how eukaryotes regulate transcription.
There is thus a need to identify and characterize the molecular mechanism of transcription regulation and thereby explain how transcription factors work. Once this mechanism is determined, any of a number of assays for identifying and detecting transcription factors can be developed. The ability to manipulate the transcription of genes is necessary to overcome many obstacles in genetic engineering and gene therapy technology and will be required to cure several human diseases.